Category Archives: Genome

Genome BC Geneskool comes to Kamloops
It #39;s all part of making science fun and relevant, said Genome BC communications and education vice-president Sally Greenwood. "We make sure to explain the sc...

By: KamloopsThisWeek

See the rest here:
Genome BC Geneskool comes to Kamloops - Video

Dr. Bart Weimer - The 100K Genome Project and Food Safety
The 100K Genome Project and Food Safety - Dr. Bart Weimer, Professor -- School of Veterinary Medicine, University of California, Davis, from the 2013 NIAA Me...

By: John Blue

Continued here:
Dr. Bart Weimer - The 100K Genome Project and Food Safety - Video

genome testing

By: Haoran Li

The rest is here:
genome testing - Video

Understand Your Genome Symposium 2013

By: IlluminaInc

Original post:
Understand Your Genome Symposium 2013 - Video

May 17, 2013 How can the Tibetan antelope live at elevations of 4,000-5,000m on the Qinghai-Tibetan Plateau? Investigators rom Qinghai University, BGI, and other institutes now provide evidence of genetic factors that may be associated with the species' adaption to harsh highland environments. The data in this work will also provide implications for studying specific genetic mechanisms and the biology of other ruminant species.

The Tibetan antelope (Pantholops hodgsonii) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. Interestingly, it is the only member of the genus Pantholops. Tibetan antelope is a medium sized antelope with the unique adaptations to against the harsh high-altitude climate. For non-native mammals such as humans, they may experience life-threatening acute mountain sickness when visiting high-altitude regions.

In this study, researchers suggest that Tibetan antelopes must have evolved exceptional mechanisms to adapt to this extremely inhospitable habitat. Using next-gen sequencing technology, they have decoded the genome of Tibetan antelope and studied the underlying genetic mechanism of high-altitude adaptations.

Through the comparison between Tibetan antelope and other plain-dwelling mammals, researchers found the Tibetan antelope had the signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission, indicating that gene categories involved in energy metabolism appear to have an important role for Tibetan antelope via efficiently providing energy in conditions of low partial pressure of oxygen (PO2).

Further research revealed that both the Tibetan antelope and the highland American pika have signals of positive selection for genes involved in DNA repair and the production of ATPase. Considering the exposure to high levels of ultraviolet radiation, positive selective genes related to DNA repair may be vital to protect the Tibetan antelope from it.

Qingle Cai, Project manager from BGI, said, "The completed genome sequence of the Tibetan antelope provides a more complete blueprint for researchers to study the genetic mechanisms of highland adaptation. This work may also open a new way to understand the adaptation of the low partial pressure of oxygen in human activities."

Share this story on Facebook, Twitter, and Google:

Other social bookmarking and sharing tools:

Story Source:

The above story is reprinted from materials provided by BGI Shenzhen.

Read more here:
Genome sequence of Tibetan antelope sheds new light on high-altitude adaptation

An enormous tree's enormous genome, genes for strong-swimming sperm and more presented May 7-11 in Cold Spring Harbor, N.Y.

An enormous tree's enormous genome, genes for strong-swimming sperm and more presented May 7-11 in Cold Spring Harbor, N.Y.

By Tina Hesman Saey

Web edition: May 16, 2013

Loblolly pine trees (shown) are used for lumber, paper and many other products. Scientists have compiled the organisms genome, the largest ever attempted.

Credit: National Park Service (NPS); U.S. Department of the Interior

A record-setting genome for a towering giant Deciphering the genome of the loblolly pine is a tall order, as is perhaps fitting for a tree that can grow to be 30 meters in height.

Researchers sequenced the conifers (Pinus taeda) approximately 24 billion bases of DNA, Steven Salzberg of Johns Hopkins University reported May 10. That surpasses the previous record holder, wheat, by more than 7 billion bases. The DNA is distributed over 12 chromosomes, each about two-thirds the size of the entire human genome.

A preliminary analysis suggests the trees may have up to 64,000 protein-coding genes, although Salzberg says the number is probably smaller. Humans have just over 22,000 protein-coding genes.

Next, the researchers will tackle the sugar pine genome. That one is even bigger, with more than 35 billion DNA bases.

Read the rest here:
News in Brief: Highlights from the Biology of Genomes meeting

GAITHERSBURG, Md.--(BUSINESS WIRE)--

OpGen, Inc. today announced that new data on the utility and application of its Whole Genome Mapping technology in the public health and health care settings will be highlighted at a company-sponsored symposium and poster presentation during the American Society for Microbiology (ASM) 113th General Meeting. The meeting is being held May 18-21, 2013 at the Colorado Convention Center in Denver. OpGen will be exhibiting at booth #1216 during the conference.

Mike Miller, Ph.D., Associate Director for Laboratory Science (Retired) for the National Center for Emerging and Zoonotic Infectious Diseases, CDC, will present new data on OpGens Whole Genome Mapping technology during a poster presentation on Monday, May 19, 2013. The poster titled Whole Genome Mapping for the Analysis of Bacterial Strains from Foodborne Outbreaks will highlight the application of the technology in the analysis of food-borne pathogens. The poster provides an overview of the utility of Whole Genome Mapping to quickly analyze and map a multi-state outbreak of Salmonella ser. Typhimurium associated with contaminated peanut products.

Additionally, OpGen will host a symposium titled Complete, High Resolution Whole Genome Mapping Applications in Public and Health Care Settings on Sunday, May 19, 2013 at 7 p.m. M.D.T. at the Hyatt Regency in Denver. The symposium will feature presentations by Dr. Miller; Jack A. Gilbert, Ph.D., principal investigator, Hospital Microbiome Project at Argonne National Laboratory; and Bart Weimer, Ph.D., Director, 100K Pathogen Genome Project, Director, BGI@Davis and Director, Genomics Integration Core at West Coast Metabolomics Center at the University of California, Davis.

About OpGen, Inc.

OpGen, Inc. is a leading innovator in rapid, accurate genomic and DNA analysis systems and services. The companys Whole Genome Mapping Technology, GenomeBuilder Software and MapIt Service provide high resolution, whole genome maps for strain typing, sequence assembly and finishing, and comparative genomics in the healthcare, public health, and life sciences markets. OpGens powerful technology dramatically improves the quality of data and time-to results by providing sequence information from single DNA molecules more rapidly and less expensively than previously possible. The company is dedicated to positively influencing individual healthcare outcomes, enhancing public health, and advancing scientific research by delivering precise, actionable information and results. OpGens customers include federal and state public health centers, hospitals, leading genomic research centers, biodefense organizations, academic institutions, clinical research organizations and biotechnology companies. For more information, visit http://www.opgen.com.

View original post here:
OpGen to Present New Data on the Application of Whole Genome Mapping in Microbial Outbreaks at the American Society ...

Public release date: 17-May-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

May 17, 2013, Shenzhen, China---- Why Tibetan antelope can live at elevations of 4,000-5,000m on the Qinghai-Tibetan Plateau? In a collaborative research published in Nature Communications, investigators from Qinghai University, BGI, and other institutes provide evidence that some genetic factors may be associated with the species' adaption to harsh highland environments. The data in this work will also provide implications for studying specific genetic mechanisms and the biology of other ruminant species.

The Tibetan antelope (Pantholops hodgsonii) is a native of the high mountain steppes and semi-desert areas of the Tibetan plateau. Interestingly, it is the only member of the genus Pantholops. Tibetan antelope is a medium sized antelope with the unique adaptations to against the harsh high-altitude climate. For non-native mammals such as humans, they may experience life-threatening acute mountain sickness when visiting high-altitude regions.

In this study, researchers suggest that Tibetan antelopes must have evolved exceptional mechanisms to adapt to this extremely inhospitable habitat. Using next-gen sequencing technology, they have decoded the genome of Tibetan antelope and studied the underlying genetic mechanism of high-altitude adaptations.

Through the comparison between Tibetan antelope and other plain-dwelling mammals, researchers found the Tibetan antelope had the signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission, indicating that gene categories involved in energy metabolism appear to have an important role for Tibetan antelope via efficiently providing energy in conditions of low partial pressure of oxygen (PO2).

Further research revealed that both the Tibetan antelope and the highland American pika have signals of positive selection for genes involved in DNA repair and the production of ATPase. Considering the exposure to high levels of ultraviolet radiation, positive selective genes related to DNA repair may be vital to protect the Tibetan antelope from it.

Qingle Cai, Project manager from BGI, said, "The completed genome sequence of the Tibetan antelope provides a more complete blueprint for researchers to study the genetic mechanisms of highland adaptation. This work may also open a new way to understand the adaptation of the low partial pressure of oxygen in human activities."

###

About BGI

Read the rest here:
The genome sequence of Tibetan antelope sheds new light on high-altitude adaptation

About Us - Genome Compiler
Learn about who we are, what we do, and how to design life.

By: GenomeCompiler

Original post:
About Us - Genome Compiler - Video

Public release date: 15-May-2013 [ | E-mail | Share ]

Contact: David Gilbert degilbert@lbl.gov DOE/Joint Genome Institute

With the publication last year of its strategic plan, "Forging the Future A Ten-Year Strategic Vision" the U.S. Department of Energy Joint Genome Institute (DOE JGI) has positioned itself to provide the most current technology and expertise to their users so that they can address pressing energy and environmental scientific challenges.

An important early step in this process is the launch of the Emerging Technologies Opportunity Program (ETOP). The primary purpose of the ETOP is to develop and support selected new technologies that DOE JGI could establish to add value to the high throughput sequencing it currently carries out for its users. The program was one of several recommendations that emerged from the DOE JGI's strategic planning as well as a complementary process carried out by DOE's Office of Biological and Environmental Research. Now, a new set of partnerships is taking shape in response to the ETOP's first call for proposals. These span the development of new scalable DNA synthesis technologies to the latest approaches to high throughput sequencing and characterization of single microbial cells from complex environmental samples.

"A core philosophy of the DOE JGI is that our suite of technical and analytical capabilities needs to evolve continuously so that the scientific achievements of our users can be maximized," said Jim Bristow, who oversees the ETOP as DOE JGI's Deputy Director of Science Programs. "This occurs by building new scientific capabilities at the DOE JGI itself, and by enlisting partners, like the ones we've identified through this program, to develop and deploy highly-specialized technologies that complement activities at our Walnut Creek facility. While state-of-the art massive-scale sequencing remains a critical component of the DOE JGI, other large-scale capabilities particularly those that will help link sequence to function will be provided to JGI users in the future," Bristow said.

When the DOE JGI was founded back in 1997 to help accelerate the Human Genome Project (HGP) effort, the partnership consisted of DOE National Laboratory and university partners. After completing the DOE's commitment to the HGP in 2004, the DOE JGI opened its doors as a national user facility advancing the frontiers of genomics for energy and environmental applications. In 2012 alone, the Institute completed over 2,600 projects.

For the first cycle of the ETOP, the DOE JGI has selected these six new partnerships:

The DOE JGI expects to commit approximately $3.5 million over the next two years to the new ETOP initiatives.

"The DOE JGI strives to integrate these expanded activities in innovative and effective ways," said Bristow. "This is critical if the biological sciences are to realize the full benefits and promise of genome sequencing."

###

Read more from the original source:
The DOE Joint Genome Institute expands capabilities via new partnerships